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Improving the Computational Efficiency of the Adaptive Biasing Force Sampling by Leveraging the Telescopic-Solvation Scheme.
Journal of Chemical Theory and Computation ( IF 5.7 ) Pub Date : 2024-12-07 , DOI: 10.1021/acs.jctc.4c01209
Diship Srivastava,Niladri Patra
Journal of Chemical Theory and Computation ( IF 5.7 ) Pub Date : 2024-12-07 , DOI: 10.1021/acs.jctc.4c01209
Diship Srivastava,Niladri Patra
The number of solvent molecules present in the system during molecular dynamics is the balancing act between the need to remove the boundary effects present in the system and the computational cost. Application of the telescopic-solvation box scheme during the estimation of the potential of mean force (PMF) can be advantageous in situations where the contribution of solvent far from the site of interest toward the whole PMF is negligible, as previously demonstrated in the case of adaptive steered molecular dynamics and umbrella sampling. This work explores the application of the telescopic-solvation box scheme during enhanced sampling by the stratified adaptive biasing force (ABF) family of methods, including ABF, extended ABF, well-tempered-metadynamics extended ABF, and multiwalker extended ABF. During this scheme, the number of water molecules differed in each stratified window, whose number depended on the value of the collective variable being sampled in that window. Two systems were used to verify the viability of the telescopic scheme: unfolding (Ala)10 peptide in water and insertion of α-tocopherol in a bilayer membrane. In the first system, the 1D and 2D PMFs obtained by the telescopic-solvation scheme matched well with the benchmark PMFs estimated with a standard solvation box. The minimal energy path connecting the α-helical and extended conformational states revealed that the unfolding process of (Ala)10 in water involved multiple closely spaced metastable states. As for the second system, the PMF, equilibrium location of α-tocopherol, and the free energy associated with the desorption and flipping of α-tocopherol obtained within the scope of the telescopic-solvation box scheme agreed with their standard solvation box values. Enhanced sampling with ABF and its variants in conjunction with the telescopic-solvation scheme results in a similar quality of the estimated PMF compared to sampling with a standard solvation box, albeit with reduced computational cost.
中文翻译:
通过利用伸缩溶剂化方案提高自适应偏置力采样的计算效率。
在分子动力学过程中,系统中存在的溶剂分子数量是消除系统中存在的边界效应的需求与计算成本之间的平衡作用。在估计平均力 (PMF) 电位时应用伸缩式溶剂化箱方案可能是有利的,因为远离感兴趣位点的溶剂对整个 PMF 的贡献可以忽略不计,如前面的自适应控制分子动力学和伞式采样所证明的那样。这项工作探讨了分层自适应偏置力 (ABF) 系列方法(包括 ABF、扩展 ABF、Well-Tempered-metadynamics 扩展 ABF 和多游行器扩展 ABF)在增强采样过程中伸缩式溶剂化箱方案的应用。在此方案中,每个分层窗口中的水分子数量不同,其数量取决于在该窗口中采样的集体变量的值。使用两个系统来验证伸缩方案的可行性:在水中展开 (Ala)10 肽和将 α-生育酚插入双层膜。在第一个系统中,通过伸缩溶剂化方案获得的 1D 和 2D PMF 与使用标准溶剂化箱估计的基准 PMF 非常匹配。连接 α 螺旋和扩展构象态的最小能量路径表明,(Ala)10 在水中的展开过程涉及多个紧密间隔的亚稳态。至于第二个系统,PMF、α-生育酚的平衡位置以及与伸缩溶剂化箱方案范围内获得的 α-生育酚的解吸和翻转相关的自由能与它们的标准溶剂化箱值一致。 与使用标准溶剂化箱进行采样相比,使用 ABF 及其变体结合伸缩溶剂化方案进行增强采样,导致估计的 PMF 质量相似,尽管计算成本降低。
更新日期:2024-12-07
中文翻译:
通过利用伸缩溶剂化方案提高自适应偏置力采样的计算效率。
在分子动力学过程中,系统中存在的溶剂分子数量是消除系统中存在的边界效应的需求与计算成本之间的平衡作用。在估计平均力 (PMF) 电位时应用伸缩式溶剂化箱方案可能是有利的,因为远离感兴趣位点的溶剂对整个 PMF 的贡献可以忽略不计,如前面的自适应控制分子动力学和伞式采样所证明的那样。这项工作探讨了分层自适应偏置力 (ABF) 系列方法(包括 ABF、扩展 ABF、Well-Tempered-metadynamics 扩展 ABF 和多游行器扩展 ABF)在增强采样过程中伸缩式溶剂化箱方案的应用。在此方案中,每个分层窗口中的水分子数量不同,其数量取决于在该窗口中采样的集体变量的值。使用两个系统来验证伸缩方案的可行性:在水中展开 (Ala)10 肽和将 α-生育酚插入双层膜。在第一个系统中,通过伸缩溶剂化方案获得的 1D 和 2D PMF 与使用标准溶剂化箱估计的基准 PMF 非常匹配。连接 α 螺旋和扩展构象态的最小能量路径表明,(Ala)10 在水中的展开过程涉及多个紧密间隔的亚稳态。至于第二个系统,PMF、α-生育酚的平衡位置以及与伸缩溶剂化箱方案范围内获得的 α-生育酚的解吸和翻转相关的自由能与它们的标准溶剂化箱值一致。 与使用标准溶剂化箱进行采样相比,使用 ABF 及其变体结合伸缩溶剂化方案进行增强采样,导致估计的 PMF 质量相似,尽管计算成本降低。